Zinc in PDB 5tt8: Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Protein crystallography data
The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide, PDB code: 5tt8
was solved by
J.K.Modak,
A.Roujeinikova,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.32 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.240,
134.400,
165.280,
90.00,
90.04,
90.00
|
R / Rfree (%)
|
19.8 /
23.1
|
Other elements in 5tt8:
The structure of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
(pdb code 5tt8). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide, PDB code: 5tt8:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 1 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:43.4
occ:0.70
|
ND1
|
A:HIS129
|
1.8
|
33.8
|
1.0
|
N4
|
A:D8W303
|
1.9
|
35.6
|
1.0
|
NE2
|
A:HIS110
|
1.9
|
29.3
|
1.0
|
NE2
|
A:HIS112
|
2.0
|
30.2
|
1.0
|
CD2
|
A:HIS110
|
2.6
|
32.2
|
1.0
|
CE1
|
A:HIS129
|
2.7
|
28.7
|
1.0
|
CD2
|
A:HIS112
|
2.8
|
35.3
|
1.0
|
O4
|
A:D8W303
|
2.9
|
29.6
|
1.0
|
S3
|
A:D8W303
|
2.9
|
37.7
|
1.0
|
CG
|
A:HIS129
|
2.9
|
32.0
|
1.0
|
CE1
|
A:HIS110
|
3.1
|
30.6
|
1.0
|
CE1
|
A:HIS112
|
3.2
|
32.4
|
1.0
|
CB
|
A:HIS129
|
3.4
|
32.7
|
1.0
|
OG1
|
A:THR191
|
3.7
|
39.8
|
1.0
|
CG
|
A:HIS110
|
3.8
|
35.0
|
1.0
|
NE2
|
A:HIS129
|
3.9
|
34.2
|
1.0
|
CD2
|
A:HIS129
|
4.0
|
33.1
|
1.0
|
C8
|
A:D8W303
|
4.0
|
30.7
|
1.0
|
ND1
|
A:HIS110
|
4.0
|
35.0
|
1.0
|
CG
|
A:HIS112
|
4.1
|
33.2
|
1.0
|
O3
|
A:D8W303
|
4.1
|
38.6
|
1.0
|
ND1
|
A:HIS112
|
4.2
|
33.8
|
1.0
|
S2
|
A:D8W303
|
4.8
|
41.3
|
1.0
|
OE1
|
A:GLU116
|
4.9
|
34.5
|
1.0
|
CA
|
A:HIS129
|
4.9
|
35.3
|
1.0
|
N3
|
A:D8W303
|
4.9
|
32.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 2 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:37.9
occ:1.00
|
NE2
|
B:HIS112
|
1.9
|
36.1
|
1.0
|
NE2
|
B:HIS110
|
1.9
|
33.5
|
1.0
|
N4
|
B:D8W303
|
2.1
|
29.9
|
1.0
|
CE1
|
B:HIS112
|
2.2
|
38.8
|
1.0
|
ND1
|
B:HIS129
|
2.4
|
34.2
|
1.0
|
CD2
|
B:HIS110
|
2.8
|
34.0
|
1.0
|
O4
|
B:D8W303
|
3.0
|
42.0
|
1.0
|
CE1
|
B:HIS110
|
3.0
|
37.8
|
1.0
|
S3
|
B:D8W303
|
3.1
|
31.1
|
1.0
|
CD2
|
B:HIS112
|
3.2
|
35.1
|
1.0
|
CG
|
B:HIS129
|
3.3
|
34.5
|
1.0
|
CE1
|
B:HIS129
|
3.4
|
30.1
|
1.0
|
ND1
|
B:HIS112
|
3.4
|
38.3
|
1.0
|
CB
|
B:HIS129
|
3.5
|
40.1
|
1.0
|
CG
|
B:HIS112
|
3.9
|
38.0
|
1.0
|
C8
|
B:D8W303
|
4.0
|
30.4
|
1.0
|
OG1
|
B:THR191
|
4.0
|
30.8
|
1.0
|
CG
|
B:HIS110
|
4.0
|
41.4
|
1.0
|
ND1
|
B:HIS110
|
4.1
|
34.6
|
1.0
|
O3
|
B:D8W303
|
4.3
|
34.8
|
1.0
|
CD2
|
B:HIS129
|
4.5
|
27.7
|
1.0
|
NE2
|
B:HIS129
|
4.5
|
24.8
|
1.0
|
OE1
|
B:GLU116
|
4.5
|
28.8
|
1.0
|
S2
|
B:D8W303
|
4.7
|
37.4
|
1.0
|
N3
|
B:D8W303
|
4.9
|
31.3
|
1.0
|
CA
|
B:HIS129
|
5.0
|
36.2
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 3 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:28.1
occ:1.00
|
NE2
|
C:HIS110
|
2.1
|
21.2
|
1.0
|
NE2
|
C:HIS112
|
2.2
|
21.7
|
1.0
|
N4
|
C:D8W303
|
2.2
|
28.3
|
1.0
|
CD2
|
C:HIS110
|
2.4
|
19.9
|
1.0
|
ND1
|
C:HIS129
|
2.4
|
20.3
|
1.0
|
CE1
|
C:HIS112
|
3.0
|
20.1
|
1.0
|
CD2
|
C:HIS112
|
3.0
|
18.8
|
1.0
|
O4
|
C:D8W303
|
3.2
|
15.2
|
1.0
|
S3
|
C:D8W303
|
3.3
|
25.3
|
1.0
|
CE1
|
C:HIS129
|
3.4
|
17.7
|
1.0
|
CE1
|
C:HIS110
|
3.4
|
19.2
|
1.0
|
CG
|
C:HIS129
|
3.4
|
18.3
|
1.0
|
CB
|
C:HIS129
|
3.7
|
19.3
|
1.0
|
CG
|
C:HIS110
|
3.7
|
19.4
|
1.0
|
OG1
|
C:THR191
|
3.8
|
23.9
|
1.0
|
ND1
|
C:HIS112
|
4.0
|
18.9
|
1.0
|
O2
|
C:GOL304
|
4.0
|
24.5
|
1.0
|
CG
|
C:HIS112
|
4.0
|
16.6
|
1.0
|
ND1
|
C:HIS110
|
4.1
|
17.5
|
1.0
|
C8
|
C:D8W303
|
4.2
|
18.3
|
1.0
|
O3
|
C:D8W303
|
4.5
|
25.1
|
1.0
|
NE2
|
C:HIS129
|
4.5
|
18.6
|
1.0
|
CD2
|
C:HIS129
|
4.5
|
17.2
|
1.0
|
C2
|
C:GOL304
|
4.8
|
19.4
|
1.0
|
CB
|
C:HIS110
|
4.9
|
22.2
|
1.0
|
CG2
|
C:THR191
|
5.0
|
18.4
|
1.0
|
CB
|
C:THR191
|
5.0
|
20.5
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 4 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:41.7
occ:0.70
|
NE2
|
D:HIS112
|
1.9
|
43.6
|
1.0
|
N4
|
D:D8W302
|
1.9
|
26.1
|
1.0
|
NE2
|
D:HIS110
|
2.0
|
42.0
|
1.0
|
O4
|
D:D8W302
|
2.7
|
44.1
|
1.0
|
CD2
|
D:HIS110
|
2.7
|
39.9
|
1.0
|
S3
|
D:D8W302
|
2.8
|
37.1
|
1.0
|
CD2
|
D:HIS112
|
2.9
|
40.2
|
1.0
|
ND1
|
D:HIS129
|
2.9
|
46.2
|
1.0
|
CE1
|
D:HIS112
|
2.9
|
45.9
|
1.0
|
CE1
|
D:HIS110
|
3.2
|
41.3
|
1.0
|
CE1
|
D:HIS129
|
3.7
|
52.5
|
1.0
|
CG
|
D:HIS129
|
3.7
|
44.9
|
1.0
|
OG1
|
D:THR191
|
3.7
|
31.0
|
1.0
|
C8
|
D:D8W302
|
3.8
|
30.9
|
1.0
|
OE2
|
D:GLU116
|
3.9
|
48.1
|
1.0
|
CB
|
D:HIS129
|
4.0
|
40.7
|
1.0
|
CG
|
D:HIS110
|
4.0
|
38.1
|
1.0
|
ND1
|
D:HIS112
|
4.0
|
52.4
|
1.0
|
CG
|
D:HIS112
|
4.0
|
44.5
|
1.0
|
O3
|
D:D8W302
|
4.1
|
37.0
|
1.0
|
ND1
|
D:HIS110
|
4.2
|
39.1
|
1.0
|
S2
|
D:D8W302
|
4.5
|
47.4
|
1.0
|
NE2
|
D:HIS129
|
4.6
|
53.8
|
1.0
|
CD2
|
D:HIS129
|
4.7
|
45.1
|
1.0
|
CD
|
D:GLU116
|
4.7
|
48.5
|
1.0
|
N3
|
D:D8W302
|
4.8
|
35.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 5 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:40.7
occ:1.00
|
NE2
|
E:HIS112
|
1.7
|
26.5
|
1.0
|
NE2
|
E:HIS110
|
1.8
|
24.3
|
1.0
|
N4
|
E:D8W303
|
2.2
|
29.9
|
0.5
|
N4
|
E:D8W303
|
2.2
|
29.9
|
0.5
|
ND1
|
E:HIS129
|
2.3
|
21.3
|
1.0
|
O3
|
E:D8W303
|
2.5
|
27.3
|
0.5
|
O3
|
E:D8W303
|
2.5
|
27.4
|
0.5
|
CE1
|
E:HIS112
|
2.5
|
21.2
|
1.0
|
CD2
|
E:HIS110
|
2.7
|
20.9
|
1.0
|
S3
|
E:D8W303
|
2.8
|
27.9
|
0.5
|
CD2
|
E:HIS112
|
2.8
|
22.4
|
1.0
|
S3
|
E:D8W303
|
2.8
|
27.6
|
0.5
|
CE1
|
E:HIS110
|
2.9
|
24.3
|
1.0
|
CE1
|
E:HIS129
|
3.1
|
22.2
|
1.0
|
CG
|
E:HIS129
|
3.2
|
23.9
|
1.0
|
CB
|
E:HIS129
|
3.6
|
22.4
|
1.0
|
ND1
|
E:HIS112
|
3.7
|
26.3
|
1.0
|
CG
|
E:HIS112
|
3.8
|
22.3
|
1.0
|
CG
|
E:HIS110
|
3.9
|
18.5
|
1.0
|
C8
|
E:D8W303
|
3.9
|
34.0
|
0.5
|
C8
|
E:D8W303
|
3.9
|
34.0
|
0.5
|
OG1
|
E:THR191
|
3.9
|
29.0
|
1.0
|
ND1
|
E:HIS110
|
3.9
|
25.1
|
1.0
|
OE1
|
E:GLU116
|
4.0
|
30.3
|
1.0
|
O4
|
E:D8W303
|
4.0
|
29.0
|
0.5
|
O4
|
E:D8W303
|
4.1
|
29.0
|
0.5
|
NE2
|
E:HIS129
|
4.2
|
22.7
|
1.0
|
CD2
|
E:HIS129
|
4.3
|
25.0
|
1.0
|
S2
|
E:D8W303
|
4.6
|
61.3
|
0.5
|
S2
|
E:D8W303
|
4.6
|
62.1
|
0.5
|
CD
|
E:GLU116
|
4.9
|
22.1
|
1.0
|
N3
|
E:D8W303
|
4.9
|
33.4
|
0.5
|
N3
|
E:D8W303
|
4.9
|
33.4
|
0.5
|
|
Zinc binding site 6 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 6 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn301
b:46.7
occ:0.70
|
NE2
|
F:HIS112
|
1.9
|
46.2
|
1.0
|
NE2
|
F:HIS110
|
2.0
|
43.2
|
1.0
|
CD2
|
F:HIS110
|
2.4
|
39.9
|
1.0
|
CE1
|
F:HIS112
|
2.8
|
50.0
|
1.0
|
CD2
|
F:HIS112
|
2.9
|
47.5
|
1.0
|
CB
|
F:HIS129
|
3.0
|
34.9
|
1.0
|
CE1
|
F:HIS110
|
3.2
|
35.3
|
1.0
|
ND1
|
F:HIS129
|
3.3
|
43.1
|
1.0
|
CG
|
F:HIS129
|
3.4
|
38.5
|
1.0
|
CG
|
F:HIS110
|
3.7
|
41.3
|
1.0
|
ND1
|
F:HIS112
|
3.9
|
48.8
|
1.0
|
CG
|
F:HIS112
|
3.9
|
48.1
|
1.0
|
ND1
|
F:HIS110
|
4.0
|
37.9
|
1.0
|
CA
|
F:HIS129
|
4.3
|
34.6
|
1.0
|
CE1
|
F:HIS129
|
4.4
|
46.0
|
1.0
|
CG2
|
F:THR191
|
4.5
|
39.6
|
1.0
|
O
|
F:HIS129
|
4.6
|
36.5
|
1.0
|
CD2
|
F:HIS129
|
4.7
|
43.4
|
1.0
|
N
|
F:HIS129
|
4.7
|
33.7
|
1.0
|
O
|
F:HIS110
|
4.8
|
39.0
|
1.0
|
OE1
|
F:GLU116
|
4.8
|
43.5
|
1.0
|
C
|
F:HIS129
|
4.9
|
32.1
|
1.0
|
CB
|
F:HIS110
|
5.0
|
38.9
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 7 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn301
b:48.3
occ:1.00
|
NE2
|
G:HIS112
|
1.8
|
30.6
|
1.0
|
NE2
|
G:HIS110
|
1.8
|
32.8
|
1.0
|
N4
|
G:D8W302
|
2.0
|
26.7
|
1.0
|
ND1
|
G:HIS129
|
2.5
|
46.1
|
1.0
|
CD2
|
G:HIS112
|
2.7
|
33.6
|
1.0
|
CD2
|
G:HIS110
|
2.7
|
34.6
|
1.0
|
CE1
|
G:HIS112
|
2.9
|
32.6
|
1.0
|
CE1
|
G:HIS110
|
3.0
|
31.0
|
1.0
|
S3
|
G:D8W302
|
3.1
|
33.3
|
1.0
|
O4
|
G:D8W302
|
3.1
|
23.8
|
1.0
|
CG
|
G:HIS129
|
3.4
|
45.8
|
1.0
|
CE1
|
G:HIS129
|
3.5
|
40.7
|
1.0
|
CB
|
G:HIS129
|
3.6
|
41.0
|
1.0
|
CG
|
G:HIS112
|
3.9
|
33.9
|
1.0
|
CG
|
G:HIS110
|
3.9
|
37.9
|
1.0
|
ND1
|
G:HIS112
|
3.9
|
30.8
|
1.0
|
ND1
|
G:HIS110
|
4.0
|
32.2
|
1.0
|
C8
|
G:D8W302
|
4.1
|
34.9
|
1.0
|
OE1
|
G:GLU116
|
4.1
|
30.5
|
1.0
|
OG1
|
G:THR191
|
4.1
|
37.8
|
1.0
|
O3
|
G:D8W302
|
4.3
|
33.3
|
1.0
|
CD2
|
G:HIS129
|
4.6
|
45.1
|
1.0
|
NE2
|
G:HIS129
|
4.6
|
43.9
|
1.0
|
S2
|
G:D8W302
|
4.8
|
48.8
|
1.0
|
CD
|
G:GLU116
|
4.9
|
26.5
|
1.0
|
N3
|
G:D8W302
|
5.0
|
35.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5tt8
Go back to
Zinc Binding Sites List in 5tt8
Zinc binding site 8 out
of 8 in the Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of the Complex of Helicobacter Pylori Alpha-Carbonic Anhydrase with Benzolamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn301
b:37.7
occ:1.00
|
NE2
|
H:HIS110
|
1.7
|
23.9
|
1.0
|
NE2
|
H:HIS112
|
1.8
|
31.2
|
1.0
|
N4
|
H:D8W302
|
1.9
|
25.3
|
1.0
|
ND1
|
H:HIS129
|
2.1
|
25.2
|
1.0
|
CD2
|
H:HIS110
|
2.5
|
27.9
|
1.0
|
CE1
|
H:HIS112
|
2.7
|
33.1
|
1.0
|
CE1
|
H:HIS110
|
2.8
|
28.9
|
1.0
|
CD2
|
H:HIS112
|
2.9
|
32.4
|
1.0
|
O3
|
H:D8W302
|
2.9
|
27.2
|
1.0
|
S3
|
H:D8W302
|
2.9
|
27.4
|
1.0
|
CE1
|
H:HIS129
|
3.0
|
27.1
|
1.0
|
CG
|
H:HIS129
|
3.2
|
22.9
|
1.0
|
CB
|
H:HIS129
|
3.6
|
29.6
|
1.0
|
CG
|
H:HIS110
|
3.7
|
30.5
|
1.0
|
OG1
|
H:THR191
|
3.7
|
30.3
|
1.0
|
ND1
|
H:HIS112
|
3.8
|
31.3
|
1.0
|
ND1
|
H:HIS110
|
3.8
|
30.3
|
1.0
|
CG
|
H:HIS112
|
4.0
|
31.6
|
1.0
|
C8
|
H:D8W302
|
4.0
|
31.6
|
1.0
|
NE2
|
H:HIS129
|
4.1
|
22.3
|
1.0
|
O4
|
H:D8W302
|
4.2
|
29.4
|
1.0
|
CD2
|
H:HIS129
|
4.2
|
23.1
|
1.0
|
OE1
|
H:GLU116
|
4.3
|
26.3
|
1.0
|
S2
|
H:D8W302
|
4.7
|
51.1
|
1.0
|
N3
|
H:D8W302
|
4.9
|
27.3
|
1.0
|
|
Reference:
J.K.Modak,
Y.C.Liu,
C.T.Supuran,
A.Roujeinikova.
Structure-Activity Relationship For Sulfonamide Inhibition of Helicobacter Pylori Alpha-Carbonic Anhydrase. J. Med. Chem. V. 59 11098 2016.
ISSN: ISSN 1520-4804
PubMed: 28002963
DOI: 10.1021/ACS.JMEDCHEM.6B01333
Page generated: Mon Oct 28 08:48:19 2024
|